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PubMed1983

Intermolecular interactions in collagen self-assembly as revealed by Fourier transform infrared spectroscopy.

When a solution of collagen molecules, at neutral pH and moderate ionic strength, is warmed from 4 degrees to 30 degrees C, a spontaneous self-assembly process takes place in which native-type collagen fibers are produced. Events occurring during thermally induced fibrillogenesis process can be monitored, in aqueous media and in real time, by Fourier transform infrared spectroscopic techniques. Tentative assignments of observed spectral bands are given.

Animals↗
PubMed1981

Cytochrome oxidase (a3) heme and copper observed by low-temperature Fourier transform infrared spectroscopy of the CO complex.

Carbon monoxide bound to iron or copper in substrate-reduced mitochondrial cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) from beef heart has been used to explore the structural interaction of the a3 heme-copper pocket at 15 K and 80 K in the dark and in the presence of visible light. The vibrational absorptions of CO measured by a Fourier transform infrared interferometer occur in the dark at 1963 cm-1, with small absorptions near 1952 cm-1, and are due to a3 heme--CO complexes. These disappear in strong visible light and are replaced by a major absorption at 2062 cm-1 and a minor one at 2043 cm-1 due to Cu--CO. Relaxation in the dark is rapid and quantitative at 210 K, but becomes negligible below 140 K. The multiple absorptions indicate structural heterogeneity of cytochrome oxidase in mitochondria. The Cu--CO absorptions (vCO) are similar to those in hemocyanin--CO complexes from molluscs (vCO - 2062 cm-1) and crustaceans (vCO = 2043 cm-1). The 2062 cm-1 Cu--CO absorption of cytochrome oxidase is split into two bands at 15 K. Analysis of spectral data suggest the presence of a very nonpolar heme--Cu pocket in which the heme-CO complex is highly ordered, but in which the Cu--CO complex is much more flexible, especially above 80 K. A function for these structures in oxygen reduction is proposed.

Animals↗
PubMed1992

Hydration of the Gly2 and Gly3 peptide oxygens of [Leu5]-enkephalin in aqueous solution as revealed by the combined use of 17O-NMR and Fourier-transform infrared spectroscopy.

Solvent-induced and temperature-induced 17O chemical shifts of [17O-Gly2, Leu5]-enkephalin and [17O-Gly3, Leu5]-enkephalin and solvent-induced spectral modifications of the amide-I' stretching vibrations of [1-13C-Gly2, Leu5]-enkephalin and [1-13C-Gly2, Leu5]-enkephalin are reported and correlated with the spectroscopic characteristics of model amides. It is demonstrated that both Gly2 and Gly3 peptide oxygens are motionally equivalent and form solvation species which are essentially monohydrated in aqueous solution, contrary to several simple amides and model peptides in which water largely forms dihydrates. It is shown that the combined use of 17O-NMR and Fourier transform infrared is a unique methodology for studying the hydration state of specific peptide oxygens in peptide hormones.

Deuterium↗
PubMed2000

Ferrielectric liquid crystal subphase studied by polarized fourier-transform infrared spectroscopy

IR dichroism and the structure of a homogeneously aligned cell of a chiral smectic antiferroelectric liquid crystal (R)-1-methylheptyl 4-(4(')-dodecyloxybiphenyl-4-ylcarbonyloxy)-3-fluorobenzoate [with acronym (R)-12OF1M7] in a ferrielectric subphase in the temperature range between the antiferroelectric phase (also referred to as Fi2) and the smectic-C*(SmC*) phase are studied using polarized Fourier transform IR spectroscopy. The polarization dependencies of the absorbance for several characteristic bands are quantitatively analyzed for different stages of the electrically induced structural transformations in the sample, including the helix unwinding and the phase transition from the ferriphase to the SmC* phase. A qualitative similarity of the voltage dependence of the normalized angular shift of the IR absorbance profile for the "chiral" carbonyl band to that of the normalized macroscopic polarization is found. The voltage dependent dichroic properties of the sample are analyzed in terms of the molecular structure and unwinding of the helical structure under an external electric field. The rotational orientational biasing of the carbonyl groups around the long molecular axis is confirmed by the spectral data. The analysis of IR dichroic data for the field induced SmC* phase is used to determine the rotational orientational distributions for the carbonyl groups.

Journal Article↗
PubMed1991

Protein secondary structure from Fourier transform infrared spectroscopy: a data base analysis.

An infrared (ir) method to determine the secondary structure of proteins in solution using the amide I region of the spectrum has been devised. The method is based on the circular dichroism (CD) matrix method for secondary structure analysis given by Compton and Johnson (L. A. Compton and W. C. Johnson, 1986, Anal. Biochem. 155, 155-167). The infrared data matrix was constructed from the normalized Fourier transform infrared spectra from 1700 to 1600 cm-1 of 17 commercially available proteins. The secondary structure matrix was constructed from the X-ray data of the seventeen proteins with secondary structure elements of helix, beta-sheet, beta-turn, and other (random). The CD and ir methods were compared by analyzing the proteins of the CD and ir databases as unknowns. Both methods produce similar results compared to structures obtained by X-ray crystallographic means with the CD slightly better for helix conformation, and the ir slightly better for beta-sheet. The relatively good ir analysis for concanavalin A and alpha-chymotrypsin indicate that the ir method is less affected by the presence of aromatic groups. The concentration of the protein and the cell path length need not be known for the ir analysis since the spectra can be normalized to the total ir intensity in the amide I region. The ir spectra for helix, beta-sheet, beta-turn, and other, as extracted from the data-base, agree with the literature band assignments. The ir data matrix and the inverse matrix necessary to analyze unknown proteins are presented.

Circular Dichroism↗
PubMedDate not supplied

Evaluation of in vivo adsorption of blood elements onto hydrogel-coated silicone rubber by scanning electron microscopy and fourier transform infrared spectroscopy.

Three hydrogel formulations consisting of 2-hydroxyethyl methacrylate (HEMA) copolymerized with N-vinyl pyrrolidone (NVP) were incorporated into silicone rubber by irradiation-induced polymerization. These coatings were chosen to represent different degrees of hydrophilicity, and they changed the hydrophobic character of the silicone rubber surface to that of hydrophilic. These composite materials and the silicone rubber comparison material were used as femoral artery-to-vein (A-V) shunts and were removed at 15 min, an approximate time representative of an initial buildup stage of blood elements on test surfaces. Data obtained by scanning electron microscopy (SEM) were used to determine the type and amount of adhering blood cells and fibrin at the time interval described. One-half of each specimen was used for Fourier Transform Infrared (FT-IR) analysis to provide a direct comparison of the relative amounts of protein present on the silicone rubber and the three hydrogel composite samples. The combined SEM and FT-IR analyses were performed on A-V samples from three dogs. Differences in the response of blood to the surfaces were found by the combined SEM and FT-IR analyses. The more hydrophilic a hydrogel grafted surface, the less fibrin and cellular elements were seen deposited on it. This is not interpreted as an indication of less reactivity, but is more likely due to thrombus buildup and a degree of subsequent embolization (a tearing of sections of the platelet matting away from a surface, revealing an area that again can be covered.

Acrylates↗
PubMed1992

Secondary structure changes stabilize the reactive-centre cleaved form of SERPINs. A study by 1H nuclear magnetic resonance and Fourier transform infrared spectroscopy.

Proteinase inhibitor members of the SERPIN superfamily are characterized by the presence of a proteolytically sensitive reactive-site loop. Cleavage within this region results in a conformational transition from an unstable "stressed" native protein to a more stable "relaxed" cleaved molecule. In order to identify the principal molecular aspects of this transition, 1H nuclear magnetic resonance (n.m.r.) and FT-IR spectroscopy were applied to the study of four SERPINs. 1H n.m.r. spectra of approximately 20 high-field ring-current-shifted methyl signals exhibited slightly different chemical shifts in the native and cleaved forms of alpha 1-antitrypsin (alpha 1-AT), alpha 1-antichymotrypsin (alpha 1-ACT) and C1 inhibitor (C1-INH), but not ovalbumin, between 20 degrees C and 90 degrees C. Ring current calculations based on crystal co-ordinates for cleaved alpha 1-AT and alpha 1-ACT and native ovalbumin showed that these signals originate from highly localized interactions between different buried residues corresponding to alpha-helix and beta-sheet segments of the SERPIN fold. The small shift changes correspond to small relative conformational side-chain rearrangements of about 0.01 nm to 0.05 nm in the protein hydrophobic core, i.e. the tertiary structure interactions in the two forms of the SERPIN fold are well-preserved, and changes in this appear unimportant for the stabilization found after reactive centre cleavage. Fourier transform infrared (FT-IR) spectroscopic studies of the amide I band showed that the native and cleaved forms of alpha 1-AT, alpha 1-ACT and C1-INH contain 28% to 36% alpha-helix and 38% to 44% beta-sheet. Second derivative FT-IR spectra using H2O and 2H2O buffers revealed very large differences in the amide I band between the native and cleaved forms of alpha 1-AT, alpha 1-ACT and C1-INH, but not for ovalbumin. The alpha-helix band was most sensitive to 1H-2H exchange, while the beta-sheet bands were not, and greater amounts of antiparallel beta-sheet were detected in the cleaved form. 1H n.m.r. showed that polypeptide amide 1H-2H exchange was greater in the native forms of alpha 1-AT, alpha 1-ACT and C1-INH than in their cleaved forms, whereas for ovalbumin it was unchanged. The FT-IR and 1H-2H exchange data show that alterations in the secondary structure are central to the stabilization of the cleaved SERPIN structure.(ABSTRACT TRUNCATED AT 400 WORDS)

Complement C1 Inactivator Proteins↗
PubMed2005

Substrate-induced conformational changes of melibiose permease from Escherichia coli studied by infrared difference spectroscopy.

Fourier transform infrared difference spectroscopy has been used to obtain information about substrate-induced structural changes of the melibiose permease (MelB) from Escherichia coli reconstituted into liposomes. Binding of the cosubstrate Na(+) gives rise to several peaks in the amide I and II regions of the difference spectrum Na(+).MelB minus H(+).MelB, that denote the presence of conformational changes in all types of secondary structures (alpha-helices, beta-sheets, loops). In addition, peaks around 1400 and at 1740-1720 cm(-1) are indicative of changes in protonation/deprotonation or in environment of carboxylic groups. Binding of the cosubstrate Li(+) produces a difference spectrum that is also indicative of conformational changes, but that is at variance as compared to that induced by Na(+) binding. To analyze the following transport steps, the melibiose permease with either H(+), Na(+), or Li(+) bound was incubated with melibiose. The difference spectra obtained by subtracting the spectrum cation.MelB from the respective complex cation.melibiose.MelB were roughly similar among them, but different from those induced by cation binding, and more intense. Therefore, major conformational changes that are induced during melibiose binding/substrate translocation, like those denoted by intense peaks at 1668 and 1645 cm(-)(1), are similar for the three cotransporting cations. Changes in the protonation state and/or in the environment of given carboxylic residues were also induced by melibiose-MelB interaction in the presence of cations.

Binding Sites↗
PubMed1991

Introduction to Fourier transform infrared spectroscopy and applications in the pharmaceutical sciences.

The applications of infrared spectroscopy to pharmaceutical sciences is small compared to the applications of infrared spectroscopy to the fields of chemistry, biology, and biochemistry. This is unfortunate because modern routine infrared spectrometers are excellent research tools that provide very high signal-to-noise, high resolution, and extensive data-manipulation computer software packages. This review summarizes basic principles of infrared spectrometers and the use of Fourier self-deconvolution.

Fourier Analysis↗
PubMed1980

Direct observation of substrate distortion by triosephosphate isomerase using Fourier transform infrared spectroscopy.

The infrared spectrum of dihydroxyacetone phosphate bound to triosephosphate isomerase has been measured. There are two carbonyl bands corresponding to the bound substrate, with an intensity ratio of about 3:1. Relative to the carbonyl absorption of dihydroxyacetone phosphate in free solution, the major band is shifted by 19 cm-1 to 1713 cm-1, providing direct evidence of enzyme-induced distortion of the substrate. This strain is probably attributable to an enzymic electrophile that polarizes the carbonyl group of the substrate and thereby promotes catalysis.

Animals↗
PubMed1988

The structure of proteins in aqueous solutions: an assessment of triose phosphate isomerase structure by Fourier-transform infrared spectroscopy.

Recent resolution enhancement and curve-fitting techniques have been applied to infrared spectra from triose phosphate isomerase in aqueous solution, in order to obtain quantitative information on its secondary structure. From our results, 57% alpha-helix, 25% beta-parallel and 10% beta-turns are predicted, in close agreement with the X-ray crystallographic data. On the other hand, measurements of band intensities, both in original and deconvolved spectra are shown to be unreliable for the quantification of secondary structures. The presence of beta-edge structure interacting with the alpha-helical barrel is described and discussed.

Carbohydrate Epimerases↗